Research workbench
Crystal structure of the SUB2-YRA1 complex in association with RNA
Analyse Crystal structure of the SUB2-YRA1 complex in association with RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SUP
- Type
- protein + RNA
- Length
- 1,214 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase SUB2; RNA annealing protein YRA1; RNA…
- EC
- 3.6.4.13
- UniProt
- Q07478, Q12159
- Ligands
- ADP, BEF, MG
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent RNA helicase SUB2 (EC 3.6.4.13) | protein | 383 | 42% helix, 17% strand | Q07478 |
| C | ATP-dependent RNA helicase SUB2 (EC 3.6.4.13) | protein | 381 | 41% helix, 17% strand | Q07478 |
| G, H | RNA annealing protein YRA1 | protein | 17 | 65% helix, 0% strand | Q12159 |
| I | RNA annealing protein YRA1 | protein | 15 | 80% helix, 0% strand | Q12159 |
| D, E, F | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | rna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.85 | 0.88 | 104 | ADP, BEF, MG |
| 2 | 340 | 0.77 | 0.88 | 46 | empty |
| 3 | 227 | 0.73 | 0.88 | 39 | ADP, BEF, MG |
| 4 | 325 | 0.67 | 0.82 | 40 | ADP, BEF, MG |
| 5 | 209 | 0.59 | 0.81 | 28 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1125 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 643 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 631 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 625 Ų buried · 12 hydrogen bonds · protein-protein
- C–I · 623 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5SUP · Crystal structure of the Sub2-Yra1 complex in association with RNA · the same entry in another collection · chain F against F, TM-score 1.00
- Q07478 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase SUB2 (Q07478) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q12159 · AlphaFold monomer V2.0 prediction for RNA annealing protein YRA1 (Q12159) · a predicted model of the same protein · chain G against A, TM-score 0.61
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q07478
- Every structure of UniProt Q12159
- Elsewhere: RCSB PDB 5SUP · PDBe 5SUP · UniProt Q07478 · UniProt Q12159
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